Cargando…

Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies

We present a set of statistical methods for the analysis of DNA methylation microarray data, which account for tumor purity. These methods are an extension of our previously developed method for purity estimation; our updated method is flexible, efficient, and does not require data from reference sa...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zheng, Xiaoqi, Zhang, Naiqian, Wu, Hua-Jun, Wu, Hao
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2017
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5267453/ https://www.ncbi.nlm.nih.gov/pubmed/28122605 http://dx.doi.org/10.1186/s13059-016-1143-5

Ejemplares similares

MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
por: Zheng, Xiaoqi, et al.
Publicado: (2014)

InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research
por: Qin, Yufang, et al.
Publicado: (2018)

Determinants of DNA yield and purity collected with buccal cell samples
por: van Wieren-de Wijer, D. B. M. A., et al.
Publicado: (2009)

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors
por: Wilkerson, Matthew D., et al.
Publicado: (2014)

Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity
por: Geeleher, Paul, et al.
Publicado: (2018)

Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution
por: Chen, Kylie, et al.
Publicado: (2022)

Gene set enrichment analysis for genome-wide DNA methylation data
por: Maksimovic, Jovana, et al.
Publicado: (2021)

PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data
por: Wang, Shudong, et al.
Publicado: (2019)

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference
por: Rahmani, Elior, et al.
Publicado: (2018)

Pancancer analysis of DNA methylation-driven genes using MethylMix
por: Gevaert, Olivier, et al.
Publicado: (2015)

ExosomePurity: tumour purity deconvolution in serum exosomes based on miRNA signatures
por: Wu, Tao, et al.
Publicado: (2023)

Improved strategy for jet‐in‐air cell sorting with high purity, yield, viability, and genome stability
por: Song, Xinghui, et al.
Publicado: (2021)

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data
por: Uzun, Yasin, et al.
Publicado: (2021)

Tumor purity adjusted beta values improve biological interpretability of high-dimensional DNA methylation data
por: Staaf, Johan, et al.
Publicado: (2022)

Estimating Temporally Variable Selection Intensity from Ancient DNA Data
por: He, Zhangyi, et al.
Publicado: (2023)

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
por: Cameron, Christopher JF, et al.
Publicado: (2020)

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
por: Liu, Yaping, et al.
Publicado: (2012)

Accounting for missing data in statistical analyses: multiple imputation is not always the answer
por: Hughes, Rachael A, et al.
Publicado: (2019)

Flux balance analysis accounting for metabolite dilution
por: Benyamini, Tomer, et al.
Publicado: (2010)

Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels
por: Manzari, Caterina, et al.
Publicado: (2020)

MethReg: estimating the regulatory potential of DNA methylation in gene transcription
por: Silva, Tiago C, et al.
Publicado: (2022)

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors
por: Williams, Justin, et al.
Publicado: (2021)

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
por: Vaisvila, Romualdas, et al.
Publicado: (2021)

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
por: Li, Jin, et al.
Publicado: (2019)

PUREE: accurate pan-cancer tumor purity estimation from gene expression data
por: Revkov, Egor, et al.
Publicado: (2023)

methyl-ATAC-seq measures DNA methylation at accessible chromatin
por: Spektor, Roman, et al.
Publicado: (2019)

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
por: Li, Bo, et al.
Publicado: (2014)

High-salt transcription from enzymatically gapped promoters nets higher yields and purity of transcribed RNAs
por: MalagodaPathiranage, Kithmie, et al.
Publicado: (2023)

TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis
por: Li, Ziyi, et al.
Publicado: (2019)

methylCC: technology-independent estimation of cell type composition using differentially methylated regions
por: Hicks, Stephanie C., et al.
Publicado: (2019)

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data
por: Fan, Yu, et al.
Publicado: (2016)

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
por: Vincent, Martin, et al.
Publicado: (2017)

Gene ontology analysis for RNA-seq: accounting for selection bias
por: Young, Matthew D, et al.
Publicado: (2010)

IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis
por: Fan, Yue, et al.
Publicado: (2019)

Optimized design and data analysis of tag-based cytosine methylation assays
por: Suzuki, Masako, et al.
Publicado: (2010)

Heat treatment of thioredoxin fusions increases the purity of α‐helical transmembrane protein constructs
por: Schenkel, Mathias, et al.
Publicado: (2021)

Identification of active regulatory regions from DNA methylation data
por: Burger, Lukas, et al.
Publicado: (2013)

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
por: Teng, Mingxiang, et al.
Publicado: (2017)

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
por: Stevens, Michael, et al.
Publicado: (2013)

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
por: Riebler, Andrea, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_ru4reiftijdfegoomjsckcri1s